LAMMPS (7 Aug 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
  using 1 OpenMP thread(s) per MPI task
# Steinhardt-Nelson bond orientational order parameters for icosahedral cluster
# W_6_hat is sensitive to icosohedral order

variable        rcut equal 1.2 # a bit bigger than LJ Rmin
variable        rcutred equal 0.75 # a bit bigger than 1/sqrt(2)

# create a perfect fcc crystallite

atom_style	atomic
boundary	s s s
lattice		fcc 1.0 # neighbors at LJ Rmin
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region		box block 0 2 0 2 0 2
create_box	1 box
Created orthogonal box = (0 0 0) to (3.1748 3.1748 3.1748)
  1 by 2 by 2 MPI processor grid
create_atoms	1 box
Created 63 atoms
  create_atoms CPU = 0.000592947 secs
mass		1 1.0

region 		centralatom sphere 1 1 1 0.0 side in
group 		centralatom region centralatom
1 atoms in group centralatom

region 		mysphere sphere 1 1 1 ${rcutred} side out
region 		mysphere sphere 1 1 1 0.75 side out
delete_atoms 	region mysphere
Deleted 50 atoms, new total = 13

# LJ potential

pair_style	lj/cut 100.0
pair_coeff	* * 1.0 1.0 100.0

# define output for central atom

compute 	qlwlhat all orientorder/atom wl/hat yes cutoff ${rcut} nnn NULL
compute 	qlwlhat all orientorder/atom wl/hat yes cutoff 1.2 nnn NULL
compute 	avql centralatom reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5]
compute 	avwlhat centralatom reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10]
variable	q6 equal c_avql[2]
variable	w6hat equal c_avwlhat[2]

compute 	mype all pe/atom
compute 	centralatompe centralatom reduce ave c_mype

# gently equilibrate the crystallite

velocity     	all create 0.001 482748
fix	     	1 all nve
neighbor	0.3 bin
neigh_modify	every 1 check no delay 0
timestep	0.003
thermo_style    custom step temp epair etotal c_centralatompe v_q6 v_w6hat
thermo		10

run		10
Neighbor list info ...
  update every 1 steps, delay 0 steps, check no
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 100.3
  ghost atom cutoff = 100.3
  binsize = 50.15, bins = 1 1 1
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
  (2) compute orientorder/atom, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 60.76 | 60.76 | 60.76 Mbytes
Step Temp E_pair TotEng c_centralatompe v_q6 v_w6hat 
       0        0.001    -3.134107   -3.1327224           -6   0.57452426 -0.013160601 
      10 0.0021821015   -3.1357444    -3.132723   -5.9994885   0.57450756 -0.013160431 
Loop time of 0.15387 on 4 procs for 10 steps with 13 atoms

Performance: 16845.410 tau/day, 64.990 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 9.7752e-06 | 1.7285e-05 | 2.9087e-05 |   0.0 |  0.01
Neigh   | 0.055218   | 0.065482   | 0.073829   |   2.9 | 42.56
Comm    | 0.0061202  | 0.018279   | 0.028283   |   6.3 | 11.88
Output  | 0.020282   | 0.020287   | 0.020298   |   0.0 | 13.18
Modify  | 2.7895e-05 | 2.8968e-05 | 2.9802e-05 |   0.0 |  0.02
Other   |            | 0.04978    |            |       | 32.35

Nlocal:    3.25 ave 4 max 2 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost:    9.75 ave 11 max 9 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs:    19.5 ave 35 max 7 min
Histogram: 2 0 0 0 0 0 0 1 0 1
FullNghs:  39 ave 48 max 24 min
Histogram: 1 0 0 0 0 1 0 0 0 2

Total # of neighbors = 156
Ave neighs/atom = 12
Neighbor list builds = 10
Dangerous builds not checked

# quench to icosehedral cluster

minimize      	1.0e-10 1.0e-6 100 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
Per MPI rank memory allocation (min/avg/max) = 112.9 | 112.9 | 112.9 Mbytes
Step Temp E_pair TotEng c_centralatompe v_q6 v_w6hat 
      10 0.0021821015   -3.1357444    -3.132723   -5.9994885   0.57450756 -0.013160431 
      20 0.0021821015   -3.1449613   -3.1419399   -5.9764731   0.57452454  -0.01316152 
      30 0.0021821015   -3.3366586   -3.3336372   -5.7717004   0.63679987  -0.16411081 
      40 0.0021821015   -3.4097262   -3.4067048   -5.6321229   0.66331761  -0.16975374 
      49 0.0021821015    -3.409754   -3.4067326   -5.6323347   0.66332496  -0.16975389 
Loop time of 0.0932837 on 4 procs for 39 steps with 13 atoms

97.2% CPU use with 4 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final = 
        -3.13574438249     -3.40975395519     -3.40975395529
  Force two-norm initial, final = 6.46606 0.000429142
  Force max component initial, final = 1.45519 0.000196446
  Final line search alpha, max atom move = 1 0.000196446
  Iterations, force evaluations = 39 98

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 5.4121e-05 | 9.0897e-05 | 0.00014281 |   0.0 |  0.10
Neigh   | 0.019662   | 0.02379    | 0.03176    |   3.0 | 25.50
Comm    | 0.0072601  | 0.014304   | 0.019575   |   3.8 | 15.33
Output  | 0.033646   | 0.033654   | 0.03368    |   0.0 | 36.08
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.02144    |            |       | 22.99

Nlocal:    3.25 ave 6 max 1 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost:    9.75 ave 12 max 7 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs:    19.5 ave 49 max 1 min
Histogram: 2 0 0 0 1 0 0 0 0 1
FullNghs:  39 ave 72 max 12 min
Histogram: 1 0 0 0 2 0 0 0 0 1

Total # of neighbors = 156
Ave neighs/atom = 12
Neighbor list builds = 5
Dangerous builds not checked

# check Q_l values

print " "
 
print "*******************************************************************"
*******************************************************************
print " "
 
print "Comparison with reference values of Q_l "
Comparison with reference values of Q_l 
print "   [Table I in W. Mickel, S. C. Kapfer,"
   [Table I in W. Mickel, S. C. Kapfer,
print "   G. E. Schroeder-Turkand, K. Mecke, "
   G. E. Schroeder-Turkand, K. Mecke, 
print "   J. Chem. Phys. 138, 044501 (2013).]"
   J. Chem. Phys. 138, 044501 (2013).]
print " "
 

variable 	q4ref equal 0.0
variable 	q6ref equal 0.663
variable 	q8ref equal 0.0
variable 	q10ref equal 0.363
variable 	q12ref equal 0.585

variable 	q4 equal c_avql[1]
variable 	q6 equal c_avql[2]
variable 	q8 equal c_avql[3]
variable 	q10 equal c_avql[4]
variable 	q12 equal c_avql[5]

print "q4     = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)"
q4     =   0.000001 delta =     0.0000
print "q6     = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)"
q6     =   0.663325 delta =     0.0003
print "q8     = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)"
q8     =   0.000002 delta =     0.0000
print "q10    = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)"
q10    =   0.362951 delta =    -0.0000
print "q12    = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)"
q12    =   0.585423 delta =     0.0004

# check W_l_hat values

print " "
 
print "Comparison with reference values of W_l_hat"
Comparison with reference values of W_l_hat
print "   [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, "
   [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, 
print "   Phys. Rev. B 28, 784 (1983).]"
   Phys. Rev. B 28, 784 (1983).]
print " "
 

variable 	w6hatref equal -0.169754
variable 	w10hatref equal -0.093967

variable 	w4hat equal c_avwlhat[1]
variable 	w6hat equal c_avwlhat[2]
variable 	w8hat equal c_avwlhat[3]
variable 	w10hat equal c_avwlhat[4]
variable 	w12hat equal c_avwlhat[5]

print "w6hat  = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)"
w6hat  =  -0.169754 delta =   0.000000
print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)"
w10hat =  -0.093968 delta =  -0.000001
print " "
 
print "*******************************************************************"
*******************************************************************
print " "
 

Total wall time: 0:00:00
